A new way to address missing data in late-stage clinical trials.

According to ICH E9(R1), defining the estimand comes before defining the analysis approach, and the strategies for addressing intercurrent events are key components of the estimand. With the composite strategy, the problem of missing data disappears, because it becomes part of the endpoint definition. It is this perspective that we adopt in addressing the problem of missing data.

Delta Inflation, Optimism Bias, and Uncertainty in Clinical Trials.

The phenomenon of delta inflation, in which design treatment effects tend to exceed observed treatment effects, has been documented in several therapeutic areas. Delta inflation has often been attributed to investigators' optimism bias, or an unwarranted belief in the efficacy of new treatments. In contrast, we argue that delta inflation may be a natural consequence of clinical equipoise, that is, genuine uncertainty about the relative benefits of treatments before a trial is initiated.

The flaw of averages: Bayes factors as posterior means of the likelihood ratio.

As an alternative to the Frequentist p-value, the Bayes factor (or ratio of marginal likelihoods) has been regarded as one of the primary tools for Bayesian hypothesis testing. In recent years, several researchers have begun to re-analyze results from prominent medical journals, as well as from trials for FDA-approved drugs, to show that Bayes factors often give divergent conclusions from those of p-values. In this paper, we investigate the claim that Bayes factors are straightforward to interpret as directly quantifying the relative strength of evidence.

Epistemic uncertainty in Bayesian predictive probabilities.

Bayesian predictive probabilities have become a ubiquitous tool for design and monitoring of clinical trials. The typical procedure is to average predictive probabilities over the prior or posterior distributions. In this paper, we highlight the limitations of relying solely on averaging, and propose the reporting of intervals or quantiles for the predictive probabilities.

Sample size formula for a win ratio endpoint.

The win ratio composite endpoint, which organizes the components of the composite hierarchically, is becoming popular in late-stage clinical trials. The method involves comparing data in a pair-wise manner starting with the endpoint highest in priority (eg, cardiovascular death). If the comparison is a tie, the endpoint next highest in priority (eg, hospitalizations for heart failure) is compared, and so on.

Assessing therapeutic responses in Kras mutant cancers using genetically engineered mouse models.

The low rate of approval of novel anti-cancer agents underscores the need for better preclinical models of therapeutic response as neither xenografts nor early-generation genetically engineered mouse models (GEMMs) reliably predict human clinical outcomes. Whereas recent, sporadic GEMMs emulate many aspects of their human disease counterpart more closely, their ability to predict clinical therapeutic responses has never been tested systematically. We evaluated the utility of two state-of-the-art, mutant Kras-driven GEMMs--one of non-small-cell lung carcinoma and another of pancreatic adenocarcinoma--by assessing responses to existing standard-of-care chemotherapeutics, and subsequently in combination with EGFR and VEGF inhibitors.

Identification of direct target genes using joint sequence and expression likelihood with application to DAF-16.

A major challenge in the post-genome era is to reconstruct regulatory networks from the biological knowledge accumulated up to date. The development of tools for identifying direct target genes of transcription factors (TFs) is critical to this endeavor. Given a set of microarray experiments, a probabilistic model called TRANSMODIS has been developed which can infer the direct targets of a TF by integrating sequence motif, gene expression and ChIP-chip data.

Endpoints for agents that slow tumor growth.

The endpoints of confirmed response and progression are widely used in oncology clinical trials. These endpoints originated at a time when agents used to treat cancer were primarily cytotoxic. Increasingly agents that are cytostatic are being investigated in combination with agents that are cytotoxic.

Regional activation of chromosomal arm 7q with and without gene amplification in taxane-selected human ovarian cancer cell lines.

Taxanes are important drugs in the treatment of ovarian and other cancers, but their efficacy is limited by intrinsic and acquired drug resistance. Expression of the multidrug transporter P-glycoprotein, encoded by the MDR1 (ABCB1) gene, is one of the causes of clinical drug resistance to taxanes. To study the mechanisms of MDR1 activation related to taxanes, we established 11 multidrug-resistant variants from six ovarian cancer cell lines by continuous exposure to either paclitaxel or docetaxel.

Tumor necrosis factor-alpha-induced protein 3 as a putative regulator of nuclear factor-kappaB-mediated resistance to O6-alkylating agents in human glioblastomas.

Purpose: Pre-existing and acquired drug resistance are major obstacles to the successful treatment of glioblastomas.

Methods: We used an integrated resistance model and genomics tools to globally explore molecular factors and cellular pathways mediating resistance to O6-alkylating agents in glioblastoma cells.

Results: We identified a transcriptomic signature that predicts a common in vitro and in vivo resistance phenotype to these agents, a proportion of which is imprinted recurrently by gene dosage changes in the resistant glioblastoma genome.